CSA had nothing to do with the Indian wars which were rampant for Decades after the Civil War. Maybe this clip about Sherman and the Yankee Controlled Federal Government to the Indians in their Race War will help you:
I will say nothing and do nothing to restrain our troops from doing what they deem proper on the spot, and will allow no more vague general charge of cruelty or inhumanity to tie their hands, but will use all the power confided in me to the end that these Indians, the enemies of our race and of our civilization, shall not . . .carry on their barbarous warfare." Sherman thus instructed Sheridan to attack without restraint, and promised to run interference against any complaints about atrocities from the East. "You may now go ahead in your own way, and I will back you with my whole authority, and stand between you and any efforts that may be attempted in your rear to restrain you purpose or check your troops."
Although Sherman had not ordered an extermination campaign in so many words, he had given Sheridan prior authorization to slaughter as many women and children as well as men Sheridan or his subordinates felt was necessary when they attacked Indian villages. However many they killed. Sherman would cover the political and media front, They were freed to do anything. At the same time, Sherman maintained personal deniability--he could assert in any public forum that he had not ordered any atrocities that might occur. Soon Grant would go to the White House, Sherman to Washington as Grant's successor, and Sheridan to Chicago to take over Sherman's role as commander of the war against the Plains Indians. pp 271 Citizen Sherman by Fellman.
The 3 Amigos and the Federal Government Race War against the Indians. O My.